Various 'omics' methods have enabled environmental probing at the molecular level and have created an important new paradigm in bioremediation design and management. Ecogenomics - the application of genomics to ecological and environmental sciences - defines phylogenetic and functional biodiversity at the DNA, RNA and protein levels. It capitalizes on this knowledge to elucidate functions and interactions of organisms at the ecosystem level in relation to ecological and evolutionary processes. Effective bioremediation of widespread halo-organic pollutants in anaerobic environments requires knowledge of catabolic potential and in situ dynamics of organohalide-respiring and co-metabolizing microorganisms. Here, we discuss the potential of ecogenomics approaches in developing high-throughput methods for detecting and monitoring organohalide respirers, and for providing improvements to selection, specificity and sensitivity of target biomarkers and their application to evaluate bioremediation strategies.